Combinations of histone deacetylase (HDAC) inhibitors (HDACi) and DNA methyltransferase (DNMT) inhibitors (DNMTi) may induce more profound clinical responses in patients with myeloid malignancies compared to DNMTi alone. However, the relationship between the clinical responses and the ability of these drug combinations to reverse transcriptional silencing of methylated genes in vitro through the reversal of promoter methylation remains uncertain. In addition to their effects on epigenetic transcriptional control, both classes of drugs can lead to DNA damage. E1905 is a randomized Phase II Intergroup trial in patients with myeloid malignancies designed to estimate clinical response rates to a novel schedule of the DNMTi 5- azacitidine (SAC), alone and in combination with the oral HDACi MS-275 to determine whether the addition of the HDACi increases the number of clinical responses or the percentage of complete and partial responses compared to the DNMT inhibitor alone. The correlative studies proposed in this application will determine whether clinical response to a DNMTi, alone or in combination with an HDACi, requires reversal of gene methylation and expression of epigenetically silenced genes. Specifically selected methylated promoters characteristically associated with MDS and AML will be studied using methylation-specific PCR to determine the frequency with which reversal of gene methylation and re-expression of these genes is associated with clinical response to SAC + MS-275. A complementary genomics-based study of methylation and methylation changes will be used to identify candidate genes and groups of genes whose methylation patterns or whose reversal of methylation may be specifically associated with and predictive of treatment response. The alternative hypothesis that the clinical effect of these drugs derives from their DNA damaging properties will also be explored: the frequency of induction of double stranded DNA breaks in response to SAC + MS-275 will be determined, and the relationship between such DNA damage and clinical response induction will be defined. Understanding of the mechanism underlying the clinical activity of these drugs in myeloid malignancies will greatly facilitate further drug development and clinical trial design as the science of epigenetics is translated to treatment for other cancers.